Will it not start at all without starting fluid? Interesting that it ran better, but you really didn't change anything, right? The injectors were not rebuilt? There could be a lot of diesel in the muffler that is still puking out, but that should clear up fairly quickly.
Unless you have access to a diesel compression gauge and the correct fittings you won't be able to do a compression check yourself. Some shops prefer to do a bleed down test using compressed air and measuring how long the cylinders will hold a certain PSI.
SV Laurie Anne
1988 Brewer 40 Pilothouse